Job ID = 6508484 SRX = SRX287906 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:28:34 prefetch.2.10.7: 1) Downloading 'SRR870095'... 2020-06-26T14:28:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:30:59 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:30:59 prefetch.2.10.7: 1) 'SRR870095' was downloaded successfully Read 18249589 spots for SRR870095/SRR870095.sra Written 18249589 spots for SRR870095/SRR870095.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:54 18249589 reads; of these: 18249589 (100.00%) were unpaired; of these: 1102786 (6.04%) aligned 0 times 13105465 (71.81%) aligned exactly 1 time 4041338 (22.14%) aligned >1 times 93.96% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2105547 / 17146803 = 0.1228 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:43:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 23:43:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:43:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:43:09: 1000000 INFO @ Fri, 26 Jun 2020 23:43:15: 2000000 INFO @ Fri, 26 Jun 2020 23:43:21: 3000000 INFO @ Fri, 26 Jun 2020 23:43:27: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:43:33: 5000000 INFO @ Fri, 26 Jun 2020 23:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 23:43:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:43:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:43:39: 6000000 INFO @ Fri, 26 Jun 2020 23:43:39: 1000000 INFO @ Fri, 26 Jun 2020 23:43:45: 7000000 INFO @ Fri, 26 Jun 2020 23:43:45: 2000000 INFO @ Fri, 26 Jun 2020 23:43:51: 8000000 INFO @ Fri, 26 Jun 2020 23:43:52: 3000000 INFO @ Fri, 26 Jun 2020 23:43:57: 9000000 INFO @ Fri, 26 Jun 2020 23:43:58: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 23:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 23:44:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:44:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:44:03: 10000000 INFO @ Fri, 26 Jun 2020 23:44:04: 5000000 INFO @ Fri, 26 Jun 2020 23:44:09: 1000000 INFO @ Fri, 26 Jun 2020 23:44:10: 11000000 INFO @ Fri, 26 Jun 2020 23:44:10: 6000000 INFO @ Fri, 26 Jun 2020 23:44:16: 2000000 INFO @ Fri, 26 Jun 2020 23:44:16: 12000000 INFO @ Fri, 26 Jun 2020 23:44:16: 7000000 INFO @ Fri, 26 Jun 2020 23:44:22: 3000000 INFO @ Fri, 26 Jun 2020 23:44:22: 8000000 INFO @ Fri, 26 Jun 2020 23:44:23: 13000000 INFO @ Fri, 26 Jun 2020 23:44:28: 4000000 INFO @ Fri, 26 Jun 2020 23:44:29: 9000000 INFO @ Fri, 26 Jun 2020 23:44:29: 14000000 INFO @ Fri, 26 Jun 2020 23:44:34: 5000000 INFO @ Fri, 26 Jun 2020 23:44:35: 10000000 INFO @ Fri, 26 Jun 2020 23:44:36: 15000000 INFO @ Fri, 26 Jun 2020 23:44:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:44:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:44:36: #1 total tags in treatment: 15041256 INFO @ Fri, 26 Jun 2020 23:44:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:44:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:44:37: #1 tags after filtering in treatment: 15041256 INFO @ Fri, 26 Jun 2020 23:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:44:37: #1 finished! INFO @ Fri, 26 Jun 2020 23:44:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:44:38: #2 number of paired peaks: 308 WARNING @ Fri, 26 Jun 2020 23:44:38: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 26 Jun 2020 23:44:38: start model_add_line... INFO @ Fri, 26 Jun 2020 23:44:38: start X-correlation... INFO @ Fri, 26 Jun 2020 23:44:38: end of X-cor INFO @ Fri, 26 Jun 2020 23:44:38: #2 finished! INFO @ Fri, 26 Jun 2020 23:44:38: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 23:44:38: #2 alternative fragment length(s) may be 3,41 bps INFO @ Fri, 26 Jun 2020 23:44:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.05_model.r WARNING @ Fri, 26 Jun 2020 23:44:38: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:44:38: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Fri, 26 Jun 2020 23:44:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:44:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:44:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:44:40: 6000000 INFO @ Fri, 26 Jun 2020 23:44:41: 11000000 INFO @ Fri, 26 Jun 2020 23:44:46: 7000000 INFO @ Fri, 26 Jun 2020 23:44:47: 12000000 INFO @ Fri, 26 Jun 2020 23:44:52: 8000000 INFO @ Fri, 26 Jun 2020 23:44:53: 13000000 INFO @ Fri, 26 Jun 2020 23:44:58: 9000000 INFO @ Fri, 26 Jun 2020 23:45:00: 14000000 INFO @ Fri, 26 Jun 2020 23:45:04: 10000000 INFO @ Fri, 26 Jun 2020 23:45:06: 15000000 INFO @ Fri, 26 Jun 2020 23:45:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:45:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:45:06: #1 total tags in treatment: 15041256 INFO @ Fri, 26 Jun 2020 23:45:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:45:07: #1 tags after filtering in treatment: 15041256 INFO @ Fri, 26 Jun 2020 23:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:45:07: #1 finished! INFO @ Fri, 26 Jun 2020 23:45:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:45:08: #2 number of paired peaks: 308 WARNING @ Fri, 26 Jun 2020 23:45:08: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 26 Jun 2020 23:45:08: start model_add_line... INFO @ Fri, 26 Jun 2020 23:45:08: start X-correlation... INFO @ Fri, 26 Jun 2020 23:45:08: end of X-cor INFO @ Fri, 26 Jun 2020 23:45:08: #2 finished! INFO @ Fri, 26 Jun 2020 23:45:08: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 23:45:08: #2 alternative fragment length(s) may be 3,41 bps INFO @ Fri, 26 Jun 2020 23:45:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.10_model.r WARNING @ Fri, 26 Jun 2020 23:45:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:45:08: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Fri, 26 Jun 2020 23:45:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:45:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:45:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:45:10: 11000000 INFO @ Fri, 26 Jun 2020 23:45:16: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:45:22: 13000000 INFO @ Fri, 26 Jun 2020 23:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.05_summits.bed INFO @ Fri, 26 Jun 2020 23:45:25: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (2145 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:45:28: 14000000 INFO @ Fri, 26 Jun 2020 23:45:34: 15000000 INFO @ Fri, 26 Jun 2020 23:45:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:45:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:45:35: #1 total tags in treatment: 15041256 INFO @ Fri, 26 Jun 2020 23:45:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:45:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:45:35: #1 tags after filtering in treatment: 15041256 INFO @ Fri, 26 Jun 2020 23:45:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:45:35: #1 finished! INFO @ Fri, 26 Jun 2020 23:45:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:45:37: #2 number of paired peaks: 308 WARNING @ Fri, 26 Jun 2020 23:45:37: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 26 Jun 2020 23:45:37: start model_add_line... INFO @ Fri, 26 Jun 2020 23:45:37: start X-correlation... INFO @ Fri, 26 Jun 2020 23:45:37: end of X-cor INFO @ Fri, 26 Jun 2020 23:45:37: #2 finished! INFO @ Fri, 26 Jun 2020 23:45:37: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 23:45:37: #2 alternative fragment length(s) may be 3,41 bps INFO @ Fri, 26 Jun 2020 23:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.20_model.r WARNING @ Fri, 26 Jun 2020 23:45:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:45:37: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Fri, 26 Jun 2020 23:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:45:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:45:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.10_summits.bed INFO @ Fri, 26 Jun 2020 23:45:57: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (1342 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:46:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287906/SRX287906.20_summits.bed INFO @ Fri, 26 Jun 2020 23:46:25: Done! pass1 - making usageList (216 chroms): 5 millis pass2 - checking and writing primary data (453 records, 4 fields): 17 millis CompletedMACS2peakCalling